Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: UNIPROT:P06889 (Mol)
 630,302 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

A PC version of three-dimensional molecular graphics package has been developed to run under MS-DOS environment on IBM PC-compatible computers equipped with a VGA graphics board. The program consists of two parts: a menu-driven interactive system module in EGA mode, and a ray-tracing module in VGA mode. In the 256-color VGA mode, ray-tracing images are represented with a 4-color map, with 64 levels for each color: 32 levels of illuminance and 32 levels of saturation. Molecular structure can be analyzed along various directions with various light sources. Ray-tracing images are also represented in a 16-color EGA mode with the half-toning method, which can display 76 gray levels for each color. To obtain good photo-realistic images in an efficient way, we have used two light sources, with an intensity ratio of 7:3, which are located in front of the top right and bottom left corners of the screen.
J Mol Graph 1992 Dec
PMID:Photorealistic image generation of molecular structure on PC screen using the ray-tracing technique. 147 94

We have developed a computer database containing information on over 1,000 human hypoxanthine guanine phosphoribosyl transferase (HPRT) mutants. Both published and unpublished data are present. The database itself is maintained in a dBASE format (.DBF) and we provide a set of programs to examine and extract information from the database. A program to input information into the database is also supplied. The database and programs are available directly from us or via remote FTP (file transfer protocol) using BITNET/INTERNET. All programs require an IBM-compatible computer, the MS-DOS operating system (version 3.3 or greater), and a hard disk with about 5 megabytes of free disk space. The purpose of the database is 1) to allow investigators to contribute their HPRT mutants directly to the database in a standardized fashion, and 2) to allow access to the entire database with a set of programs that allows manipulation and extraction of data. For example, using our programs it is possible to i) order the database by base pair position, ii) examine only information regarding mutagenesis by a particular agent, iii) search for a particular author, iv) create a report which contains selected portions of the database, the report can be printed or saved as a file. The database will be updated every several months and distributed.
Environ Mol Mutagen 1992
PMID:Human HPRT mutant database: software for data entry and retrieval. 150 31

A cost effective color graphics representation of molecular electrostatic potential surfaces employing the cumulative atomic or bond multipole moments has been described. A general description of the method used to obtain cumulative multipole moments directly from ab-initio wavefunctions is given, along with an outline of the algorithm for generating electrostatic potential surfaces in the molecular graphics programs MOL17 (FORTRAN 77, Silicon Graphics 3130 and 4D series workstations) and PCMCAMM (Turbo Pascal, IBM PC and PS/2 computers). Examples are given that illustrate the convergence of the multiple expansion, the degree of basis-set dependence compensated by the use of higher atomic moments, and the effect of placing additional expansion centers along the bonds.
J Mol Graph 1991 Jun
PMID:Efficient method for the generation and display of electrostatic potential surfaces from ab-initio wavefunctions. 176 44

The SMILE program runs under MS-DOS on IBM PC AT-compatible computers equipped with the SM640 or the PG640 Matrox graphic board. The program allows real-time three-dimensional (3D) animation and modeling of several isolated molecules that can be built from scratch, manipulated interactively and compared by superimposition. SMILE enables users to compute atomic partial charges, molecular surface area, molecular volume, electrostatic and nonbonded potential energies. PLUTO, ORTEP, and MMP2 input files are set up automatically. The program also provides simple access to crystal packing by real-time animation of the unit cell contents, interactive inspection of the relevant stereochemical parameters and fragment manipulation within the unit cell. SMILE animates stereo views and produces beautiful shaded 3D images (8 colors, 32 shades each) of molecules in many different styles--stick, ball-and-stick, CPK (space filling), and transparent CPK with backbone.
J Mol Graph 1989 Sep
PMID:SMILE--shaded molecular imaging on low-cost equipment. 248 56

Our molecular modeling software package, MORPHEUS, allows the study of the interactions between biologically active molecules and their receptors. The package is capable of exploring the multidimensional conformational space accessible to each molecule of the data set under study. By specifying distance constraints or hypothetical receptor binding points, the package is able to filter the biologically accessible conformations of each active compound and deduce a three-dimensional model of the binding sites consistent with the properties of the agonists (or antagonists) under scrutiny. The electrostatic potentials in the environment of a putative binding site can also be investigated using the MORPHEUS package. The molecular modeling module CRYS-X, which is written in FORTRAN 77 for IBM PC machines, is capable of building, displaying and manipulating molecules.
J Mol Graph 1989 Sep
PMID:Morpheus: a conformation-activity relationships and receptor modeling package. 256 36

We have used an algorithm from the pattern recognition theory "generalized portrait" to find a distinguishing vector for Escherichia coli promoters. We have made an attempt to solve closely linked problems for choosing significant signs of that signal, multiple alignment and for calculation of the recognition vector (matrix). The promoters with known strength have been ranged with this vector. The analysis of the occurrence of predicted promoters has been carried out. The promoters search program for IBM-compatible computers is available from the authors.
Mol Biol (Mosk)
PMID:[Pattern recognition in the computer analysis of nucleotide sequences]. 269 77

The article describes the vectors data base and the software for its use (the VECTOR-PC system). At present the prototype versions of data base and VECTOR-PC exist and are in test exploitation. The original data base entry format contains 17 main fields for specific genetic engineering information. The VECTOR-PC system includes programs for data base search and support, and also the "genetic engineering designer", which allows the user to design his own hypothetic structures from the objects of data base and to receive detailed information about them. The system is destined for IBM PC or compatible computers.
Mol Biol (Mosk)
PMID:[An computer information system for genetic engineering]. 277 Jul 35

A program (PREDITOP) for predicting the location of antigenic regions (or epitopes) on proteins is described. This program and the associated ones are written in Turbo Pascal and run on IBM-PC compatibles. The program contains 22 normalized scales, corresponding to hydrophilicity, accessibility, flexibility, or secondary structure propensities. New scales are easily implemented. An hydrophobic moment procedure has also been implemented in order to determine amphiphilic helices. The program generates a result file where the values represent a particular physicochemical aspect of the studied protein. PREDITOP can display one or several result files by simple graphical super-imposition. Curve combinations can be done by the ADDITIO or MULTIPLI routines which create a new result file by adding or multiplying previously calculated files representing several propensities. The program is useful and efficient for identifying potential antigenic regions in a protein with the aim of raising antibodies against synthesized peptides which cross-react with the native protein.
J Mol Graph 1993 Sep
PMID:PREDITOP: a program for antigenicity prediction. 750 82

Mutations at the human hypoxanthine-guanine phosphoribosyl transferase gene (hprt) are currently of great interest because mutations at this locus are being used as a biomonitor of human mutagenic exposure. Not only can somatic hprt mutants arising in vivo in humans be recovered and sequenced, but there is also a considerable body of information about the in vitro mutational spectra of different carcinogens at this locus. Previously, we reported the creation of a computerized database containing DNA-sequence information on human hprt mutants (Cariello et al. (1992) Environ. Mol. Mutagen., 20, 81-83). In the present manuscript, software for the analysis of mutations in the hprt database is described. Numerous routines have been developed for the analysis of single-base substitutions, including programs to (i) determine if two mutational spectra are different, (ii) display the number of mutations and mutable sites in each exon, (iii) determine if mutations show a DNA-strand bias, (iv) determine the frequency of transitions and transversions, (v) display the number and kind of mutations observed at each base in the coding region, (vi) perform nearest-neighbor analysis and (vii) display mutable amino acids in the hprt protein. The software runs only on IBM-compatible machines with MS-DOS. The software and hprt database is freely available via the INTERNET using remote file-transfer protocol. These programs simplify the analysis of the rapidly increasing information about hprt mutation. The programs permit the facile comparison between in vitro and in vivo data, as well as the identification of mutational patterns that may be of importance to experimenters using hprt as a biomonitor and and of importance to researchers studying mechanisms of mutation.
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PMID:Software for the analysis of mutations at the human hprt gene. 751 Aug 30

ANTHEPROT is a fully interactive graphics program devoted to the analysis of the sequences and structures of proteins. This program, originally developed to facilitate the protein sequence analysis coupled with multiple alignments and predicted secondary structures of proteins, now comprises a powerful 3D module to display and handle macromolecular structures. All the methods that were previously integrated into ANTHEPROT are now directly coupled with a 3D window that provides the user all the classic features of a molecular modeling package. Indeed, it allows real-time rotation and translation of 3D structures with many kinds of models in depth-cueing mode (space filling, backbone, wire models, main chain, and ribbons), selections (atom type, residue type, segments, and chain), color-coding systems (amino acid properties, predicted or observed secondary structures, temperature B factor, and subunits), geometric calculations (Ramachandran plot, distances, and angles), and fitting molecules. Stereo views are possible as well as HPGL standard files. A module specifically devoted to the determination of 3D structures using nuclear magnetic resonance is also available. This major release of our program for IBM rs6000 workstations is available by anonymous ftp to ibcp.fr for academic institutions.
J Mol Graph 1995 Jun
PMID:ANTHEPROT 2.0: a three-dimensional module fully coupled with protein sequence analysis methods. 757 48


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